|
| Status |
Public on Apr 17, 2018 |
| Title |
F3_BPA_sample1 |
| Sample type |
SRA |
| |
|
| Source name |
Needle-dissected gonads of adult worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
treatment: BPA 100uM
|
| Treatment protocol |
Worms were exposed to BPA 100uM or DMSO 0.1% or water for 48 hours at the P0 and adult worms at the F3 were then processed for germline dissection.
|
| Growth protocol |
Worms were maintained on NGM plates streaked with OP50 E. coli and all experiments were performed at 20°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from needle-dissected gonads of F3 adult worms in 4 replicates in each treatment group (BPA or DMSO exposed or water). The dissected germlines were processed through the NucleoSpin RNA XS, Macherey Nagel kit. cDNA was synthesized using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing, amplified 10X, and purified using agentcourt AMPure beads.
Nextera XT Library Prep Kit was used to prepare the sequencing libraries from 1 ng of cDNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
The dissected germlines were processed through the NucleoSpin RNA XS, Macherey Nagel kit. cDNA was synthesized using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing, amplified 10X, and purified using agentcourt AMPure beads. Nextera XT Library Prep Kit was used to prepare the sequencing libraries from 1 ng of cDNA. Single-end sequencing at 50 bp length was performed on an Illumina Hiseq 4000 system.
|
| Data processing |
HISAT was used to align the RNA-Seq reads against the C.elegans genome to discover the locations from which the reads originated and to determine the transcript splice sites.
StringTie was used to assemble the RNA-seq alignments into potential transcripts.
Reads Per Kilobase of transcript per Million (RPKM) for each transcript were obtained by Ballgown tool and used as the expression measure.
Genome_build: UCSC ce10
Supplementary_files_format_and_content: Transcription abundances in terms of the RPKM measure of the expressed transcripts in each sample were obtained by using Ballgown R tool.
|
| |
|
| Submission date |
Apr 17, 2018 |
| Last update date |
Apr 18, 2018 |
| Contact name |
Zeyneb Kurt |
| E-mail(s) |
zeyneb@ucla.edu
|
| Organization name |
University of California Los Angeles
|
| Department |
Integrative Biology and Physiology
|
| Lab |
Allard lab and Yang Lab
|
| Street address |
2000 Terasaki Life Sciences Bldg 610 Charles E. Young Drive East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE113266 |
The memory of environmental chemical exposure in C. elegans is dependent on the Jumonji demethylases jmjd-2 and jmjd-3/utx-1 |
|
| Relations |
| BioSample |
SAMN08942441 |
| SRA |
SRX3947894 |
